RetrogeneDB ID: retro_slyc_87

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 6:45450060..45450304(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g069520.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_87
GTTGGTATACAAGATCTTCCTATAGATTACCACGACTTTATAGTTATCATCTTCGACGTCTATGGTGCCATGTTAATTAT
CAAATGCAAGATTTGCTTGTGATTTGTTATTATATTAGGTGTGCAATCTATTGCTAACATAAAAAAATATGAAAAATGAT
TTTTAGCAAATCTCAACGGCTATGATGTTTGGTATCACGGGTCTCATGACAAACTACTTGGGTGTTAGTCCCTGGGCAAG
CAAG

Alignment

ORF - retro_slyc_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 77.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAPQDLPIDYSGFIAVICGVFGAMF--RYKICSWLAIIFSAQSLANMRN-MENDLKQISMAMMFGIMGLM
          V..QDLPIDY..FI..I..V.GAM.....KIC....II...QS.AN....M.ND..QIS.AMMFGI.GLM
Retrocopy VGIQDLPIDYHDFIVIIFDVYGAMLIIKCKICL*FVIILGVQSIANXXX>MKNDF*QISTAMMFGITGLM

Parental  TNYLGVGPRGSK
          TNYLGV.P..SK
Retrocopy TNYLGVSPWASK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum lycopersicum was not studied using ChIP-Seq data.

EST

Solanum lycopersicum was not studied using EST data.

TSS

Solanum lycopersicum was not studied using FANTOM5 data.

Lab

retro_slyc_87 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum lycopersicum does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc06g069520.2	4 retrocopies	retro_slyc_65, retro_slyc_85, retro_slyc_86, retro_slyc_87 ,